Gallery
Here we show usage examples of the LoVis4u command-line interface. For description of parameters and modes shown on this page visit the Example-driven guide page.
Sample data & Configuration files
The necessary sample data as well as adjustable tool configuration files are provided by lovis4u at the post-install step with the command:
lovis4u --data This copies the lovis4u_data folder to your working directory.
Also important to describe the set of editable configuration files with parameters already adjusted for different tasks and page layout:
- A4p1 - adjusted for one-column portrait A4 page layout. Figure width - 90mm.
- A4p2 - adjusted for two-column portrait A4 page layout. Figure width - 190mm.
- A4L - adjusted for landscape A4 page layout. Figure width - 240mm.
- standard - flexible width length, scale - 0.05 mm per nucleotide with minimal width - 80mm.
A4 page layout examples
The full-length visualisation of loci
Miltiple sequences
Visualisation with homology lines and category colours. Figure size: two-column of A4 page publication layout (190mm width).
Visualisation with homology lines and category colours. Compact one-column A4 page figure without labelling of conserved proteins (90mm width).
lovis4u -gff lovis4u_data/guide/gff_files -hl --set-category-colour \
--show-first-feature-label-for -c A4p1
One sequence
Visualisation of a single sequence with highlighted protein groups of homologues by different colours. Two-column A4 page publication layout (190mm width).
lovis4u -gff lovis4u_data/guide/single_gff_file -hl --set-category-colour -c A4p2 \
--set-group-colour-for conserved
Visualisation of user-defined regions
Visualisation of user-defined regions, one region per locus. One-column A4 page layout (90mm width).
lovis4u -gff lovis4u_data/guide/gff_files -c A4p1 --locus-annotation-file lovis4u_data/guide/locus_annotation_table_demo_2.tsv \
-cl-off -hl --set-category-colour
Visualisation of user-defined regions, multiple regions per locus.
lovis4u -gff lovis4u_data/guide/gff_files -hl -o lovis4u_output_m_loci \
--locus-annotation-file lovis4u_data/guide/locus_annotation_table_demo_1.tsv -cl-off -llp left -slt
Visualisation of the Basel collection of phages
For demonstration of LoVis4u's capabilities (and because it is fun), I applied it to the entire Basel collection of 78 Escherichia coli phages (see Maffei et.al. PLOS Biology).
LoVis4u PDF file of the visualisation
Raster image
This run also highlights one of LoVis4u key features—its ability to detect clusters of similar proteomes within the input data. Beyond visualisation, LoVis4u generates a matrix of pairwise proteome similarity (see the pipeline description page). The visualisation of this matrix for the Basel collection appears as follows:
